Created
September 17, 2021 11:00
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No output when streaming files from stding to bbtools [tadpole]: problematic case
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cat o10to12_test_TTCACCGGTCTTGCTCCGTCCTGATAGC_temp.fastq | tadpole.sh in=stdin.fastq out=from_stdin.fa k=80 mode=correct overwrite=True bm1=1 bm2=1 t=1 -Xmx6g mincontig=auto mincountseed=1 rcomp=f | |
/gnu/store/60inp2szi6c7fbdq9nkgn7dz3pvlf8zl-openjdk-11.28-jdk/bin/java -ea -Xmx6g -Xms6g -cp /gnu/store/f7q0xsx6wkrag1skhkbammjqx9i28xkz-bbmap-38.90/share/java/BBTools.jar assemble.Tadpole in=stdin.fastq out=from_stdin.fa k=80 mode=correct overwrite=True bm1=1 bm2=1 t=1 -Xmx6g mincontig=auto mincountseed=1 rcomp=f | |
Executing assemble.Tadpole2 [in=stdin.fastq, out=from_stdin.fa, k=80, mode=correct, overwrite=True, bm1=1, bm2=1, t=1, -Xmx6g, mincontig=auto, mincountseed=1, rcomp=f] | |
Version 38.90 | |
Using 1 threads. | |
Executing ukmer.KmerTableSetU [in=stdin.fastq, out=from_stdin.fa, k=80, mode=correct, overwrite=True, bm1=1, bm2=1, t=1, -Xmx6g, mincontig=auto, mincountseed=1, rcomp=f] | |
Set threads to 1 | |
K was changed from 80 to 78 | |
Initial: | |
Ways=31, initialSize=128000, prefilter=f, prealloc=f | |
Memory: max=6442m, total=6442m, free=6436m, used=6m | |
Initialization Time: 0.066 seconds. | |
Loading kmers. | |
Estimated kmer capacity: 131792503 | |
After table allocation: | |
Memory: max=6442m, total=6442m, free=6321m, used=121m | |
After loading: | |
Memory: max=6442m, total=6442m, free=6316m, used=126m | |
Input: 119 reads 26894 bases. | |
Unique Kmers: 1277 | |
Load Time: 0.120 seconds. | |
Reads Processed: 119 0.99k reads/sec | |
Bases Processed: 26894 0.22m bases/sec | |
Extending/error-correcting/discarding. | |
After extending reads: | |
Memory: max=6442m, total=6442m, free=6312m, used=130m | |
Input: 0 reads 0 bases. | |
Output: 0 reads 0 bases. | |
Errors detected: 0 | |
Errors corrected: 0 (0 reassemble) | |
Reads with errors detected: 0 (NaN%) | |
Reads fully corrected: 0 (NaN% of detected) | |
Reads partly corrected: 0 (NaN% of detected) | |
Rollbacks: 0 (NaN% of detected) | |
Extend/error-correct time: 0.015 seconds. | |
Total Time: 0.225 seconds. | |
Reads Processed: 0 0.00k reads/sec | |
Bases Processed: 0 0.00m bases/sec | |
$ head from_stdin.fa | |
$ |
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